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Sample GSM364514 Query DataSets for GSM364514
Status Public on Sep 08, 2009
Title Illumina sequenced synthetic miRNA sample A
Sample type SRA
 
Source name sample A
Organism Homo sapiens
Characteristics sample: synthetic miRNA
Biomaterial provider Integrated DNA Technologies
Treatment protocol n/a
Growth protocol n/a
Extracted molecule other
Extraction protocol n/a
 
Library strategy OTHER
Library source transcriptomic
Library selection other
Instrument model Illumina Genome Analyzer
 
Description n/a
Data processing The GAPipeline-1.0 was used starting from the IPAR-1.01 calculated intensities.
First the data sets are screened for the sequence of the 5' adapter (We sometime observed that parts of the 5' adapter can be cloned instead of a small RNA insert) with the same method than described below using the last 10 bases of this adapter. This was not observed for your samples so all reads were processed for the 3prime adapter location and removal.
The adapter sequences were trimmed in 3 steps:
1) The 21nt adapter sequence is used, which permits to identify “inserts” of 15nt or less.
2) If no adapter sequence was found, in successive steps the last base of the adapter was removed and the sequence was searched at the end of the reads. The minimum adapter size of 6 bases permits identifying inserts of up to 30 bases.
3) Finally the remaining reads are search for notexact matches of the adapter. The first 4 bases of the adapter were searched within the full reads sequences and at least 75% of the following bases must be identical to the adapter sequence (max 31 bp).
 
Submission date Jan 26, 2009
Last update date Jun 11, 2013
Contact name Hanni Willenbrock
E-mail(s) hanni@cbs.dtu.dk
Phone +45 45 66 09 85
Organization name DTU
Department Center for Biological Sequence Analysis
Street address Kemikalievej, bygning 208
City Kgs. Lyngby
ZIP/Postal code 2800
Country Denmark
 
Platform ID GPL9052
Series (1)
GSE14511 Quantification of synthetic miRNAs
Relations
BioSample SAMN02195508

Data table header descriptions
SEQUENCE
Concentration concentration of the sequence in amol/ul
COUNT number of times sequenced

Data table
SEQUENCE Concentration COUNT
hsa-let-7e* 376.470588235294 382
hsa-let-7g 376.470588235294 69070
hsa-miR-125a-5p 376.470588235294 216
hsa-miR-139-5p 376.470588235294 343
hsa-miR-181d 376.470588235294 17918
hsa-miR-182* 376.470588235294 2630
hsa-miR-193a-3p 376.470588235294 239
hsa-miR-197 376.470588235294 141
hsa-miR-222 376.470588235294 19057
hsa-miR-24-2* 376.470588235294 2424
hsa-miR-302a 376.470588235294 74
hsa-miR-30e 376.470588235294 127
hsa-miR-335* 376.470588235294 109
hsa-miR-33a 376.470588235294 3816
hsa-miR-33b* 376.470588235294 217
hsa-miR-342-3p 376.470588235294 695
hsa-miR-361-5p 376.470588235294 7374
hsa-miR-432 376.470588235294 20601
hsa-miR-449b 376.470588235294 6573
hsa-miR-485-5p 376.470588235294 227867

Total number of rows: 744

Table truncated, full table size 21 Kbytes.




Supplementary file Size Download File type/resource
GSM364514.zip.gz 118.4 Mb (ftp)(http) ZIP
Processed data included within Sample table
Raw data provided as supplementary file

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